Below, we first show an aggregation of the latest version of FNGS for our respective post-processing pipelines:
require(Discriminability)
## Loading required package: Discriminability
signal_overall <- c()
ids_overall <- c()
cpac_graphs_overall <- c()
cpac_ids_overall <- c()
dataset_overall <- c()
require(Discriminability)
inpath <- 'C:/Users/ebrid/Documents/R/fngs_merge/BNU1/roi_timeseries/aal-2mm/'
tsnames <- list.files(inpath, pattern="\\.rds", full.names=TRUE)
scan_pos = 3
tsobj <- open_timeseries(tsnames, sub_pos=scan_pos, exclude = TRUE)
## [1] "opening timeseries..."
signal <- tsobj[[1]]
ids <- tsobj[[3]]
signal_overall <- c(signal_overall, signal)
ids_overall <- c(ids_overall, tsobj$dataset)
cpac_inpath <- 'C:/Users/ebrid/Documents/R/CPAC_results/BNU1/FSL_frf_nsc_ngs_des/'
cpac_tsnames <- list.files(cpac_inpath, pattern="\\.graphml", full.names=TRUE)
scan_pos = 2
cpac_graobj <- open_graphs(cpac_tsnames, sub_pos=scan_pos)
## [1] "opening graphs..."
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cpac_graphs <- cpac_graobj[[1]]
cpac_ids <- cpac_graobj[[3]]
cpac_graphs_overall <- c(cpac_graphs_overall, cpac_graphs)
ids_overall <- c(ids_overall, cpac_graobj$dataset)
ts1 = signal[[1]]
title = paste('Timeseries plot for subject', ids[1])
print(plot_timeseries(ts1, title=title))
## Warning: package 'reshape2' was built under R version 3.3.3
## Warning: package 'ggplot2' was built under R version 3.3.3
#### FNGS Correlation Matrix
title = paste('Correlation plot for subject', ids[1])
print(plot_square(abs(cor(ts1)), title=title, legend="corr"))
title = paste('Correlation plot for subject', ids[1])
print(plot_square(cpac_graphs[[1]], title=title, legend="corr"))
td <- time_discr(signal, ids, rank=FALSE)
## [1] "computing hellinger distances and densities..."
print(td$combinedplot)
## NULL
tdr <- time_discr(signal, ids, rank=TRUE)
## [1] "computing hellinger distances and densities..."
print(tdr$combinedplot)
## NULL
cpac_td <- time_discr(cpac_graphs, cpac_ids, rank=FALSE, graphs = TRUE)
## [1] "computing hellinger distances and densities..."
print(cpac_td$combinedplot)
## NULL
cpac_tdr <- time_discr(cpac_graphs, cpac_ids, rank=TRUE, graphs = TRUE)
## [1] "computing hellinger distances and densities..."
print(cpac_tdr$combinedplot)
## NULL
collection <- data.frame(dataset='BNU1',
postprocessing=c('fngs_corr', 'fngs_rcorr',
'cpac_corr', 'cpac_rcorr'),
discr=c(td$d, tdr$d, cpac_td$d, cpac_tdr$d))
inpath <- 'C:/Users/ebrid/Documents/R/fngs_2mm_0503/DC1/aal-2mm/'
tsnames <- list.files(inpath, pattern="\\.rds", full.names=TRUE)
scan_pos = 2
tsobj <- open_timeseries(tsnames, sub_pos=scan_pos, exclude = TRUE)
## [1] "opening timeseries..."
signal <- tsobj[[1]]
ids <- tsobj[[3]]
signal_overall <- c(signal_overall, signal)
ids_overall <- c(ids_overall, tsobj$dataset)
cpac_inpath <- 'C:/Users/ebrid/Documents/R/CPAC_results/DC1/FSL_frf_nsc_ngs_aal/'
cpac_tsnames <- list.files(cpac_inpath, pattern="\\.graphml", full.names=TRUE)
scan_pos = 2
cpac_graobj <- open_graphs(cpac_tsnames, sub_pos=scan_pos)
## [1] "opening graphs..."
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cpac_graphs <- cpac_graobj[[1]]
cpac_ids <- cpac_graobj[[3]]
cpac_graphs_overall <- c(cpac_graphs_overall, cpac_graphs)
ids_overall <- c(ids_overall, cpac_graobj$dataset)
ts1 = signal[[1]]
title = paste('Timeseries plot for subject', ids[1])
print(plot_timeseries(ts1, title=title))
#### FNGS Correlation Matrix
title = paste('Correlation plot for subject', ids[1])
print(plot_square(abs(cor(ts1)), title=title, legend="corr"))
title = paste('Correlation plot for subject', ids[1])
print(plot_square(cpac_graphs[[1]], title=title, legend="corr"))
td <- time_discr(signal, ids, rank=FALSE)
## [1] "computing hellinger distances and densities..."
print(td$combinedplot)
## NULL
tdr <- time_discr(signal, ids, rank=TRUE)
## [1] "computing hellinger distances and densities..."
print(tdr$combinedplot)
## NULL
cpac_td <- time_discr(cpac_graphs, cpac_ids, rank=FALSE, graphs = TRUE)
## [1] "computing hellinger distances and densities..."
print(cpac_td$combinedplot)
## NULL
cpac_tdr <- time_discr(cpac_graphs, cpac_ids, rank=TRUE, graphs = TRUE)
## [1] "computing hellinger distances and densities..."
print(cpac_tdr$combinedplot)
## NULL
collection <- rbind(collection, data.frame(dataset='DC1',
postprocessing=c('fngs_corr', 'fngs_rcorr',
'cpac_corr', 'cpac_rcorr'),
discr=c(td$d, tdr$d, cpac_td$d, cpac_tdr$d)))
inpath <- 'C:/Users/ebrid/Documents/R/fngs_2mm_0503/HNU1/aal-2mm/'
tsnames <- list.files(inpath, pattern="\\.rds", full.names=TRUE)
scan_pos = 2
tsobj <- open_timeseries(tsnames, sub_pos=scan_pos, exclude = TRUE)
## [1] "opening timeseries..."
signal <- tsobj[[1]]
ids <- tsobj[[3]]
signal_overall <- c(signal_overall, signal)
ids_overall <- c(ids_overall, tsobj$dataset)
cpac_inpath <- 'C:/Users/ebrid/Documents/R/CPAC_results/HNU1/FSL_frf_nsc_ngs_aal/'
cpac_tsnames <- list.files(cpac_inpath, pattern="\\.graphml", full.names=TRUE)
scan_pos = 2
cpac_graobj <- open_graphs(cpac_tsnames, sub_pos=scan_pos)
## [1] "opening graphs..."
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cpac_graphs <- cpac_graobj[[1]]
cpac_ids <- cpac_graobj[[3]]
cpac_graphs_overall <- c(cpac_graphs_overall, cpac_graphs)
ids_overall <- c(ids_overall, cpac_graobj$dataset)
ts1 = signal[[1]]
title = paste('Timeseries plot for subject', ids[1])
print(plot_timeseries(ts1, title=title))
#### FNGS Correlation Matrix
title = paste('Correlation plot for subject', ids[1])
print(plot_square(abs(cor(ts1)), title=title, legend="corr"))
title = paste('Correlation plot for subject', ids[1])
print(plot_square(cpac_graphs[[1]], title=title, legend="corr"))
td <- time_discr(signal, ids, rank=FALSE)
print(td$combinedplot)
tdr <- time_discr(signal, ids, rank=TRUE)
## [1] "computing hellinger distances and densities..."
print(tdr$combinedplot)
## NULL
cpac_td <- time_discr(cpac_graphs, cpac_ids, rank=FALSE, graphs = TRUE)
## [1] "computing hellinger distances and densities..."
print(cpac_td$combinedplot)
## NULL
cpac_tdr <- time_discr(cpac_graphs, cpac_ids, rank=TRUE, graphs = TRUE)
## [1] "computing hellinger distances and densities..."
print(cpac_tdr$combinedplot)
## NULL
collection <- rbind(collection, data.frame(dataset='HNU1',
postprocessing=c('fngs_corr', 'fngs_rcorr',
'cpac_corr', 'cpac_rcorr'),
discr=c(td$d, tdr$d, cpac_td$d, cpac_tdr$d)))
inpath <- 'C:/Users/ebrid/Documents/R/fngs_2mm_0503/NYU1/aal-2mm/'
tsnames <- list.files(inpath, pattern="\\.rds", full.names=TRUE)
scan_pos = 2
tsobj <- open_timeseries(tsnames, sub_pos=scan_pos, exclude = TRUE)
## [1] "opening timeseries..."
signal <- tsobj[[1]]
ids <- tsobj[[3]]
signal_overall <- c(signal_overall, signal)
ids_overall <- c(ids_overall, tsobj$dataset)
cpac_inpath <- 'C:/Users/ebrid/Documents/R/CPAC_results/NYU1/FSL_frf_nsc_ngs_aal/'
cpac_tsnames <- list.files(cpac_inpath, pattern="\\.graphml", full.names=TRUE)
scan_pos = 2
cpac_graobj <- open_graphs(cpac_tsnames, sub_pos=scan_pos)
## [1] "opening graphs..."
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cpac_graphs <- cpac_graobj[[1]]
cpac_ids <- cpac_graobj[[3]]
cpac_graphs_overall <- c(cpac_graphs_overall, cpac_graphs)
ids_overall <- c(ids_overall, cpac_graobj$dataset)
ts1 = signal[[1]]
title = paste('Timeseries plot for subject', ids[1])
print(plot_timeseries(ts1, title=title))
#### FNGS Correlation Matrix
title = paste('Correlation plot for subject', ids[1])
print(plot_square(abs(cor(ts1)), title=title, legend="corr"))
title = paste('Correlation plot for subject', ids[1])
print(plot_square(cpac_graphs[[1]], title=title, legend="corr"))
td <- time_discr(signal, ids, rank=FALSE)
## [1] "computing hellinger distances and densities..."
print(td$combinedplot)
## NULL
tdr <- time_discr(signal, ids, rank=TRUE)
## [1] "computing hellinger distances and densities..."
print(tdr$combinedplot)
## NULL
cpac_td <- time_discr(cpac_graphs, cpac_ids, rank=FALSE, graphs = TRUE)
## [1] "computing hellinger distances and densities..."
print(cpac_td$combinedplot)
## NULL
cpac_tdr <- time_discr(cpac_graphs, cpac_ids, rank=TRUE, graphs = TRUE)
## [1] "computing hellinger distances and densities..."
print(cpac_tdr$combinedplot)
## NULL
collection <- rbind(collection, data.frame(dataset='NYU1',
postprocessing=c('fngs_corr', 'fngs_rcorr',
'cpac_corr', 'cpac_rcorr'),
discr=c(td$d, tdr$d, cpac_td$d, cpac_tdr$d)))
inpath <- 'C:/Users/ebrid/Documents/R/fngs_2mm_0503/SWU4/aal-2mm/'
tsnames <- list.files(inpath, pattern="\\.rds", full.names=TRUE)
scan_pos = 2
tsobj <- open_timeseries(tsnames, sub_pos=scan_pos, exclude = TRUE)
## [1] "opening timeseries..."
signal <- tsobj[[1]]
ids <- tsobj[[3]]
signal_overall <- c(signal_overall, signal)
ids_overall <- c(ids_overall, tsobj$dataset)
cpac_inpath <- 'C:/Users/ebrid/Documents/R/CPAC_results/SWU4/FSL_frf_nsc_ngs_aal/'
cpac_tsnames <- list.files(cpac_inpath, pattern="\\.graphml", full.names=TRUE)
scan_pos = 2
cpac_graobj <- open_graphs(cpac_tsnames, sub_pos=scan_pos)
## [1] "opening graphs..."
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cpac_graphs <- cpac_graobj[[1]]
cpac_ids <- cpac_graobj[[3]]
cpac_graphs_overall <- c(cpac_graphs_overall, cpac_graphs)
ids_overall <- c(ids_overall, cpac_graobj$dataset)
ts1 = signal[[1]]
title = paste('Timeseries plot for subject', ids[1])
print(plot_timeseries(ts1, title=title))
#### FNGS Correlation Matrix
title = paste('Correlation plot for subject', ids[1])
print(plot_square(abs(cor(ts1)), title=title, legend="corr"))
title = paste('Correlation plot for subject', ids[1])
print(plot_square(cpac_graphs[[1]], title=title, legend="corr"))
td <- time_discr(signal, ids, rank=FALSE)
## [1] "computing hellinger distances and densities..."
print(td$combinedplot)
## NULL
tdr <- time_discr(signal, ids, rank=TRUE)
## [1] "computing hellinger distances and densities..."
print(tdr$combinedplot)
## NULL
cpac_td <- time_discr(cpac_graphs, cpac_ids, rank=FALSE, graphs = TRUE)
## [1] "computing hellinger distances and densities..."
print(cpac_td$combinedplot)
## NULL
cpac_tdr <- time_discr(cpac_graphs, cpac_ids, rank=TRUE, graphs = TRUE)
print(cpac_tdr$combinedplot)
inpath <- 'C:/Users/ebrid/Documents/R/fngs_merge/BNU2/roi_timeseries/desikan-2mm/'
tsnames <- list.files(inpath, pattern="\\.rds", full.names=TRUE)
scan_pos = 3
tsobj <- open_timeseries(tsnames, sub_pos=scan_pos, exclude = TRUE)
signal <- tsobj[[1]]
ids <- tsobj[[3]]
signal_overall <- c(signal_overall, signal)
ids_overall <- c(ids_overall, tsobj$dataset)
cpac_inpath <- 'C:/Users/ebrid/Documents/R/CPAC_results/BNU2/FSL_frf_nsc_ngs_des/'
cpac_tsnames <- list.files(cpac_inpath, pattern="\\.graphml", full.names=TRUE)
scan_pos = 2
cpac_graobj <- open_graphs(cpac_tsnames, sub_pos=scan_pos)
cpac_graphs <- cpac_graobj[[1]]
cpac_ids <- cpac_graobj[[3]]
cpac_graphs_overall <- c(cpac_graphs_overall, cpac_graphs)
ids_overall <- c(ids_overall, cpac_graobj$dataset)
ts1 = signal[[1]]
title = paste('Timeseries plot for subject', ids[1])
print(plot_timeseries(ts1, title=title))
title = paste('Correlation plot for subject', ids[1])
print(plot_square(abs(cor(ts1)), title=title, legend="corr"))
title = paste('Correlation plot for subject', ids[1])
print(plot_square(cpac_graphs[[1]], title=title, legend="corr"))
td <- time_discr(signal, ids, rank=FALSE)
print(td$combinedplot)
tdr <- time_discr(signal, ids, rank=TRUE)
print(tdr$combinedplot)
cpac_td <- time_discr(cpac_graphs, cpac_ids, rank=FALSE, graphs = TRUE)
print(cpac_td$combinedplot)
cpac_tdr <- time_discr(cpac_graphs, cpac_ids, rank=TRUE, graphs = TRUE)
print(cpac_tdr$combinedplot)
collection <- rbind(collection, data.frame(dataset='HNU1',
postprocessing=c('fngs_corr', 'fngs_rcorr',
'cpac_corr', 'cpac_rcorr'),
discr=c(td$d, tdr$d, cpac_td$d, cpac_tdr$d)))
collection$dataset <- factor(collection$dataset)
collection$postprocessing <- factor(collection$postprocessing)
summaryfig_fng <- ggplot(collection, aes(x=postprocessing, y=discr, color=dataset)) +
geom_point(size=4) +
ggtitle('Comparing Discriminability over 4 reference datasets using different postprocessing techniques')
print(summaryfig_fng)
summaryfig_fng <- ggplot(collection, aes(x=postprocessing, y=discr, fill=postprocessing)) +
geom_violin() +
geom_boxplot(width=0.1) +
ggtitle('Comparing Discriminability over 4 reference datasets using different postprocessing techniques')
print(summaryfig_fng)